United Kingdom

Row

New cases

New tests

Row

Hospital patients

ICU patients

New deaths

New deaths per million

Row

People partially vaccinated (1st dose)

People fully vaccinated (2nd dose)

Hungary

Row

New cases

New tests

Row

Hospital patients

ICU patients (no data available)

New deaths

New deaths per million

Row

People partially vaccinated (1st dose)

People fully vaccinated (2nd dose)

---
title: "COVID-19 Pandemic"
output: 
  flexdashboard::flex_dashboard:
    orientation: rows
    social: menu
    source_code: embed
---

```{r setup, include=FALSE}
library(dygraphs)
library(xts)
library(lubridate)
library(dplyr)
library(tidyr)

### Data sources: 
### Our World In Data https://ourworldindata.org/coronavirus 
### Johns Hopkins Coronavirus Resource Center https://github.com/govex/COVID-19/tree/master/data_tables/vaccine_data/global_data 

covid <- read.csv(url("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv"))

uk_covid <- covid %>%
  filter(location == "United Kingdom")

hun_covid <- covid %>%
  filter(location == "Hungary")


vax <- read.csv(url("https://raw.githubusercontent.com/govex/COVID-19/master/data_tables/vaccine_data/global_data/time_series_covid19_vaccine_global.csv"))

hun_vax <- vax %>%
  filter(Country_Region == "Hungary")
```


United Kingdom
=======================================================================

Row
-----------------------------------------------------------------------

### New cases

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 7:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_cases, order.by = uk_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New tests

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 27:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_tests, order.by = uk_covid_sub$date)
names(data) <- c("New tests")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### Hospital patients

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 21:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$hosp_patients, order.by = uk_covid_sub$date)
names(data) <- c("Hospital patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### ICU patients

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 19:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$icu_patients, order.by = uk_covid_sub$date)
names(data) <- c("ICU patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 10:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_deaths, order.by = uk_covid_sub$date)
names(data) <- c("New deaths")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths per million

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 16:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$new_deaths_per_million, order.by = uk_covid_sub$date)
names(data) <- c("New deaths per million")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### People partially vaccinated (1st dose)

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$people_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People partially vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

### People fully vaccinated (2nd dose)

```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))

uk_covid_sub$date <- ymd(uk_covid_sub$date)

str(uk_covid_sub)

data <- xts(x = uk_covid_sub$people_fully_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People fully vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


Hungary
=======================================================================

Row
-----------------------------------------------------------------------

### New cases

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 7:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_cases, order.by = hun_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New tests

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 27:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_tests, order.by = hun_covid_sub$date)
names(data) <- c("New tests")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

Row
-----------------------------------------------------------------------

### Hospital patients

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 21:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$hosp_patients, order.by = hun_covid_sub$date)
names(data) <- c("Hospital patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### ICU patients (no data available)

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 19:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$icu_patients, order.by = hun_covid_sub$date)
names(data) <- c("ICU patients")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 10:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_deaths, order.by = hun_covid_sub$date)
names(data) <- c("New deaths")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


### New deaths per million

```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 16:59))

hun_covid_sub$date <- ymd(hun_covid_sub$date)

str(hun_covid_sub)

data <- xts(x = hun_covid_sub$new_deaths_per_million, order.by = hun_covid_sub$date)
names(data) <- c("New deaths per million")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```


Row
-----------------------------------------------------------------------

### People partially vaccinated (1st dose)

```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)

str(hun_vax)

data <- xts(x = hun_vax$People_partially_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People partially vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```

### People fully vaccinated (2nd dose)

```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)

str(hun_vax)

data <- xts(x = hun_vax$People_fully_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People fully vaccinated")
```

```{r}
dygraph(data) %>%
  dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
  dyCrosshair(direction = "vertical") %>%
  dyLegend(show = "always") %>%
  dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
  dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
  dyRangeSelector() 
```